Turns out the bolts were in a bad bind. I got them out intact.
I have the vehicle supported on jackstands using the tubes on the sliders. The weight of the vehicle is twisting the frame a bit causing the bind. I got it handled.
The trans is out and on solid ground. I removed the harness connectors from the trans not up behind the heads. After the trans was out and I had a nice clear look around in the tunnel, I found out that the connectors from the ECM and the wire harness I got with the M5 are completely different.
The stock ends are square, and the M5 harness is round, I don't know what I am going to do for now, so I cleaned up and closed shop.
I decided to try to get the trans out leaving the exhaust on. The 3" body lift made this possible. It was tight, but doable. A simple prybar under the lip of the bell housing, and lowering the trans tail shaft got it on top of the exhaust. Jacked it up and over the rest of the exhaust and pulled the trans back and dropped down.
I had to leave the torque converter on for this, since I am not returning the auto back in it, I didn't really give 2 hoots if I messed the trans seal or not. Turns out it didn't do any damage to the seal after all.